Comprehensive analysis of transcriptome-wide N6-methyladenosine methylomes in the Barrett's esophagus in rats

As the most abundant RNA modification, N6-methyladenosine (m6A) methylation plays crucial roles in various diseases. The aim of this study is to comprehensively map the landscape of the mRNA m6A modification pattern in Barrett's esophagus (BE) in order to find key genes and potential therapy for BE and even esophageal adenocarcinoma (EAC).

Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-sequencing (RNA-seq) were performed to compare the difference in mRNA m6A methylation and differentially expressed mRNAs between BE and normal control (NC) tissues. Bioinformatics analysis was used to describe the m6A modification pattern and specific genes in BE and NC tissues.

Through MeRIP-seq, we obtained m6A methylation profiling in BE and NC tissues. In total, 11,026 unique peaks were detected in the BE groups, whereas 8564 unique peaks were detected in the NC groups. Peaks were primarily enriched within CDS with GGACU motifs and most of the peaks were within 1000 bp in width. Moreover, functional enrichment analysis demonstrated that hypermethylated and hypomethylated genes were significantly enriched in coronavirus disease pathway, calcium signaling pathway and MAPK signaling pathways. Furthermore, PPI network was conducted and 18 hub genes were identified via STRING database and Cystoscope. Among them, ACTA1, CDC20, CKM, KIF20a, MYH11, TPM2, MYL9, DES, TNNT3 were overexpressed in EAC in the GEPIA gene bank and TPM1, KIF20a impaired patients' survival in the Kaplan-Meier plotter database. Finally, functional enrichment analysis demonstrated that co-expressed genes of TPM1 were significantly enriched in calcium signaling pathway, cGMP-PKG signaling pathway and PI3K-Akt signaling pathway.

Our study is the first to perform comprehensive and transcriptome-wide maps to identify the potential roles played by m6A methylation in BE, which widely involved in oxidative stress. This foresees a guiding role in revealing the molecular mechanism of m6A-mediated genes that govern the pathogenesis and progression of BE and EAC.